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Volumn 9, Issue 5, 2013, Pages 313-318

A single-molecule dissection of ligand binding to a protein with intrinsic dynamics

Author keywords

[No Author keywords available]

Indexed keywords

BIOTIN; MALTOSE BINDING PROTEIN; STREPTAVIDIN;

EID: 84879069952     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.1213     Document Type: Article
Times cited : (96)

References (45)
  • 1
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • Henzler-Wildman, K. & Kern, D. Dynamic personalities of proteins. Nature 450, 964-972 (2007).
    • (2007) Nature , vol.450 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 2
    • 77956501272 scopus 로고    scopus 로고
    • A transient and low-populated protein-folding intermediate at atomic resolution
    • Korzhnev, D.M., Religa, T.L., Banachewicz, W., Fersht, A.R. & Kay, L.E. A transient and low-populated protein-folding intermediate at atomic resolution. Science 329, 1312-1316 (2010).
    • (2010) Science , vol.329 , pp. 1312-1316
    • Korzhnev, D.M.1    Religa, T.L.2    Banachewicz, W.3    Fersht, A.R.4    Kay, L.E.5
  • 3
    • 80052401629 scopus 로고    scopus 로고
    • Solution structure of a minor and transiently formed state of a T4 lysozyme mutant
    • Bouvignies, G. et al. Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 477, 111-114 (2011).
    • (2011) Nature , vol.477 , pp. 111-114
    • Bouvignies, G.1
  • 4
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr, D.D., Nussinov, R. & Wright, P.E. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 5, 789-796 (2009).
    • (2009) Nat. Chem. Biol , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 5
    • 0036815758 scopus 로고    scopus 로고
    • NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis
    • Akke, M. NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis. Curr. Opin. Struct. Biol. 12, 642-647 (2002).
    • (2002) Curr. Opin. Struct. Biol , vol.12 , pp. 642-647
    • Akke, M.1
  • 7
    • 77958160823 scopus 로고    scopus 로고
    • Dynamics connect substrate recognition to catalysis in protein kinase A
    • Masterson, L.R. et al. Dynamics connect substrate recognition to catalysis in protein kinase A. Nat. Chem. Biol. 6, 821-828 (2010).
    • (2010) Nat. Chem. Biol , vol.6 , pp. 821-828
    • Masterson, L.R.1
  • 8
    • 84857190619 scopus 로고    scopus 로고
    • Evidence for dynamics in proteins as a mechanism for ligand dissociation
    • Carroll, M.J. et al. Evidence for dynamics in proteins as a mechanism for ligand dissociation. Nat. Chem. Biol. 8, 246-252 (2012).
    • (2012) Nat. Chem. Biol , vol.8 , pp. 246-252
    • Carroll, M.J.1
  • 9
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder, H., Sligar, S.G. & Wolynes, P.G. The energy landscapes and motions of proteins. Science 254, 1598-1603 (1991).
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 10
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai, C.J., Kumar, S., Ma, B. & Nussinov, R. Folding funnels, binding funnels, and protein function. Protein Sci. 8, 1181-1190 (1999).
    • (1999) Protein Sci , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 11
    • 33748557507 scopus 로고    scopus 로고
    • Recent successes of the energy landscape theory of protein folding and function
    • Wolynes, P.G. Recent successes of the energy landscape theory of protein folding and function. Q. Rev. Biophys. 38, 405-410 (2005).
    • (2005) Q. Rev. Biophys , vol.38 , pp. 405-410
    • Wolynes, P.G.1
  • 12
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland, D.E. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 44, 98-104 (1958).
    • (1958) Proc. Natl. Acad. Sci. USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 13
    • 1342302339 scopus 로고    scopus 로고
    • Conformational changes associated with protein-protein interactions
    • Goh, C.S., Milburn, D. & Gerstein, M. Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol. 14, 104-109 (2004).
    • (2004) Curr. Opin. Struct. Biol , vol.14 , pp. 104-109
    • Goh, C.S.1    Milburn, D.2    Gerstein, M.3
  • 14
    • 0035875870 scopus 로고    scopus 로고
    • Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy
    • Evenäs, J. et al. Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. J. Mol. Biol. 309, 961-974 (2001).
    • (2001) J. Mol. Biol , vol.309 , pp. 961-974
    • Evenäs, J.1
  • 15
    • 77956944744 scopus 로고    scopus 로고
    • Conformational changes and ligand recognition of Escherichia coli D-xylose binding protein revealed
    • Sooriyaarachchi, S., Ubhayasekera, W., Park, C. & Mowbray, S.L. Conformational changes and ligand recognition of Escherichia coli D-xylose binding protein revealed. J. Mol. Biol. 402, 657-668 (2010).
    • (2010) J. Mol. Biol , vol.402 , pp. 657-668
    • Sooriyaarachchi, S.1    Ubhayasekera, W.2    Park, C.3    Mowbray, S.L.4
  • 16
    • 69549120472 scopus 로고    scopus 로고
    • Conformational selection or induced fit: A flux description of reaction mechanism
    • Hammes, G.G., Chang, Y.C. & Oas, T.G. Conformational selection or induced fit: a flux description of reaction mechanism. Proc. Natl. Acad. Sci. USA 106, 13737-13741 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 13737-13741
    • Hammes, G.G.1    Chang, Y.C.2    Oas, T.G.3
  • 17
    • 79958136745 scopus 로고    scopus 로고
    • A role for both conformational selection and induced fit in ligand binding by the LAO protein
    • Silva, D.A., Bowman, G.R., Sosa-Peinado, A. & Huang, X. A role for both conformational selection and induced fit in ligand binding by the LAO protein. PLoS Comput. Biol. 7, e1002054 (2011).
    • (2011) PLoS Comput. Biol , vol.7
    • Silva, D.A.1    Bowman, G.R.2    Sosa-Peinado, A.3    Huang, X.4
  • 18
    • 77957231785 scopus 로고    scopus 로고
    • Induced fit, conformational selection and independent dynamic segments: An extended view of binding events
    • Csermely, P., Palotai, R. & Nussinov, R. Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem. Sci. 35, 539-546 (2010).
    • (2010) Trends Biochem. Sci , vol.35 , pp. 539-546
    • Csermely, P.1    Palotai, R.2    Nussinov, R.3
  • 19
    • 29344466944 scopus 로고    scopus 로고
    • Conformation coupled enzyme catalysis: Single-molecule and transient kinetics investigation of dihydrofolate reductase
    • Antikainen, N.M., Smiley, R.D., Benkovic, S.J. & Hammes, G.G. Conformation coupled enzyme catalysis: single-molecule and transient kinetics investigation of dihydrofolate reductase. Biochemistry 44, 16835-16843 (2005).
    • (2005) Biochemistry , vol.44 , pp. 16835-16843
    • Antikainen, N.M.1    Smiley, R.D.2    Benkovic, S.J.3    Hammes, G.G.4
  • 20
    • 36749083505 scopus 로고    scopus 로고
    • Illuminating the mechanistic roles of enzyme conformational dynamics
    • Hanson, J.A. et al. Illuminating the mechanistic roles of enzyme conformational dynamics. Proc. Natl. Acad. Sci. USA 104, 18055-18060 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 18055-18060
    • Hanson, J.A.1
  • 21
    • 0026493924 scopus 로고
    • Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis
    • Sharff, A.J., Rodseth, L.E., Spurlino, J.C. & Quiocho, F.A. Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. Biochemistry 31, 10657-10663 (1992).
    • (1992) Biochemistry , vol.31 , pp. 10657-10663
    • Sharff, A.J.1    Rodseth, L.E.2    Spurlino, J.C.3    Quiocho, F.A.4
  • 22
    • 35548976322 scopus 로고    scopus 로고
    • Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR
    • Tang, C., Schwieters, C.D. & Clore, G.M. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 449, 1078-1082 (2007).
    • (2007) Nature , vol.449 , pp. 1078-1082
    • Tang, C.1    Schwieters, C.D.2    Clore, G.M.3
  • 23
    • 79958863650 scopus 로고    scopus 로고
    • Free-energy landscapes of protein domain movements upon ligand binding
    • Kondo, H.X., Okimoto, N., Morimoto, G. & Taiji, M. Free-energy landscapes of protein domain movements upon ligand binding. J. Phys. Chem. B 115, 7629-7636 (2011).
    • (2011) J. Phys. Chem. B , vol.115 , pp. 7629-7636
    • Kondo, H.X.1    Okimoto, N.2    Morimoto, G.3    Taiji, M.4
  • 24
    • 0034863015 scopus 로고    scopus 로고
    • Manipulation of ligand binding affinity by exploitation of conformational coupling
    • Marvin, J.S. & Hellinga, H.W. Manipulation of ligand binding affinity by exploitation of conformational coupling. Nat. Struct. Biol. 8, 795-798 (2001).
    • (2001) Nat. Struct. Biol , vol.8 , pp. 795-798
    • Marvin, J.S.1    Hellinga, H.W.2
  • 25
    • 0242331659 scopus 로고    scopus 로고
    • The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy
    • Millet, O., Hudson, R.P. & Kay, L.E. The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy. Proc. Natl. Acad. Sci. USA 100, 12700-12705 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 12700-12705
    • Millet, O.1    Hudson, R.P.2    Kay, L.E.3
  • 26
    • 79851474946 scopus 로고    scopus 로고
    • Intrinsic Z-DNA is stabilized by the conformational selection mechanism of Z-DNA-binding proteins
    • Bae, S., Kim, D., Kim, K.K., Kim, Y.G. & Hohng, S. Intrinsic Z-DNA is stabilized by the conformational selection mechanism of Z-DNA-binding proteins. J. Am. Chem. Soc. 133, 668-671 (2011).
    • (2011) J. Am. Chem. Soc , vol.133 , pp. 668-671
    • Bae, S.1    Kim, D.2    Kim, K.K.3    Kim, Y.G.4    Hohng, S.5
  • 27
    • 77957903226 scopus 로고    scopus 로고
    • Single-molecule three-color FRET with both negligible spectral overlap and long observation time
    • Lee, S., Lee, J. & Hohng, S. Single-molecule three-color FRET with both negligible spectral overlap and long observation time. PLoS ONE 5, e12270 (2010).
    • (2010) PLoS ONE , vol.5
    • Lee, S.1    Lee, J.2    Hohng, S.3
  • 28
    • 56149121056 scopus 로고    scopus 로고
    • A nano-positioning system for macromolecular structural analysis
    • Muschielok, A. et al. A nano-positioning system for macromolecular structural analysis. Nat. Methods 5, 965-971 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 965-971
    • Muschielok, A.1
  • 29
    • 70350348011 scopus 로고    scopus 로고
    • NMR spectroscopy brings invisible protein states into focus
    • Baldwin, A.J. & Kay, L.E. NMR spectroscopy brings invisible protein states into focus. Nat. Chem. Biol. 5, 808-814 (2009).
    • (2009) Nat. Chem. Biol , vol.5 , pp. 808-814
    • Baldwin, A.J.1    Kay, L.E.2
  • 30
    • 27744499156 scopus 로고    scopus 로고
    • Intrinsic dynamics of an enzyme underlies catalysis
    • Eisenmesser, E.Z. et al. Intrinsic dynamics of an enzyme underlies catalysis. Nature 438, 117-121 (2005).
    • (2005) Nature , vol.438 , pp. 117-121
    • Eisenmesser, E.Z.1
  • 31
    • 79953823548 scopus 로고    scopus 로고
    • A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
    • Bhabha, G. et al. A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332, 234-238 (2011).
    • (2011) Science , vol.332 , pp. 234-238
    • Bhabha, G.1
  • 33
    • 33747049527 scopus 로고    scopus 로고
    • Complementarity of ensemble and single-molecule measures of protein motion: A relaxation dispersion NMR study of an enzyme complex
    • Vallurupalli, P. & Kay, L.E. Complementarity of ensemble and single-molecule measures of protein motion: a relaxation dispersion NMR study of an enzyme complex. Proc. Natl. Acad. Sci. USA 103, 11910-11915 (2006).
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 11910-11915
    • Vallurupalli, P.1    Kay, L.E.2
  • 34
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr, D.D., McElheny, D., Dyson, H.J. & Wright, P.E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313, 1638-1642 (2006).
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 35
    • 36849048228 scopus 로고    scopus 로고
    • Intrinsic motions along an enzymatic reaction trajectory
    • Henzler-Wildman, K.A. et al. Intrinsic motions along an enzymatic reaction trajectory. Nature 450, 838-844 (2007).
    • (2007) Nature , vol.450 , pp. 838-844
    • Henzler-Wildman, K.A.1
  • 36
    • 82455171948 scopus 로고    scopus 로고
    • Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein
    • Bucher, D., Grant, B.J. & McCammon, J.A. Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry 50, 10530-10539 (2011).
    • (2011) Biochemistry , vol.50 , pp. 10530-10539
    • Bucher, D.1    Grant, B.J.2    McCammon, J.A.3
  • 37
    • 77749286394 scopus 로고    scopus 로고
    • Ligand-free open-closed transitions of periplasmic binding proteins: The case of glutamine-binding protein
    • Bermejo, G.A., Strub, M.P., Ho, C. & Tjandra, N. Ligand-free open-closed transitions of periplasmic binding proteins: the case of glutamine-binding protein. Biochemistry 49, 1893-1902 (2010).
    • (2010) Biochemistry , vol.49 , pp. 1893-1902
    • Bermejo, G.A.1    Strub, M.P.2    Ho, C.3    Tjandra, N.4
  • 38
    • 0027235488 scopus 로고
    • Three-dimensional structures of the periplasmic lysine/arginine/ ornithine-binding protein with and without a ligand
    • Oh, B.H. et al. Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand. J. Biol. Chem. 268, 11348-11355 (1993).
    • (1993) J. Biol. Chem , vol.268 , pp. 11348-11355
    • Oh, B.H.1
  • 39
    • 25144472137 scopus 로고    scopus 로고
    • Conformational equlibria and free energy profiles for the allosteric transition of the ribose-binding protein
    • Ravindranathan, K.P., Gallicchio, E. & Levy, R.M. Conformational equlibria and free energy profiles for the allosteric transition of the ribose-binding protein. J. Mol. Biol. 353, 196-210 (2005).
    • (2005) J. Mol. Biol , vol.353 , pp. 196-210
    • Ravindranathan, K.P.1    Gallicchio, E.2    Levy, R.M.3
  • 40
    • 0028002085 scopus 로고
    • The 1.9 Å X-ray structure of a closed unliganded form of the periplasmic glucose/galactose receptor from Salmonella typhimurium
    • Flocco, M.M. & Mowbray, S.L. The 1.9 Å X-ray structure of a closed unliganded form of the periplasmic glucose/galactose receptor from Salmonella typhimurium. J. Biol. Chem. 269, 8931-8936 (1994).
    • (1994) J. Biol. Chem , vol.269 , pp. 8931-8936
    • Flocco, M.M.1    Mowbray, S.L.2
  • 41
    • 70349823496 scopus 로고    scopus 로고
    • Structural analysis of the choline-binding protein ChoX in a semi-closed and ligand-free conformation
    • Oswald, C., Smits, S.H., Hoing, M., Bremer, E. & Schmitt, L. Structural analysis of the choline-binding protein ChoX in a semi-closed and ligand-free conformation. Biol. Chem. 390, 1163-1170 (2009).
    • (2009) Biol. Chem , vol.390 , pp. 1163-1170
    • Oswald, C.1    Smits, S.H.2    Hoing, M.3    Bremer, E.4    Schmitt, L.5
  • 42
    • 44449134820 scopus 로고    scopus 로고
    • A practical guide to single-molecule FRET
    • Roy, R., Hohng, S. & Ha, T. A practical guide to single-molecule FRET. Nat. Methods 5, 507-516 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 507-516
    • Roy, R.1    Hohng, S.2    Ha, T.3
  • 43
    • 41449108157 scopus 로고    scopus 로고
    • An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments
    • Aitken, C.E., Marshall, R.A. & Puglisi, J.D. An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys. J. 94, 1826-1835 (2008).
    • (2008) Biophys. J , vol.94 , pp. 1826-1835
    • Aitken, C.E.1    Marshall, R.A.2    Puglisi, J.D.3
  • 44
    • 65249090946 scopus 로고    scopus 로고
    • Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis
    • Weikl, T.R. & von Deuster, C. Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis. Proteins 75, 104-110 (2009).
    • (2009) Proteins , vol.75 , pp. 104-110
    • Weikl, T.R.1    Von Deuster, C.2


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